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Henríquez T, Hsu JS, Hernandez JS, Kuppermann S, Eder M, Jung H. Contribution of Uncharacterized Target Genes of MxtR/ErdR to Carbon Source Utilization by Pseudomonas putida KT2440. Microbiol Spectr 2023; 11:e0292322. [PMID: 36511656 PMCID: PMC9927547 DOI: 10.1128/spectrum.02923-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
MxtR/ErdR is a two-component system that has been previously described as a regulator of the utilization of acetate in Vibrio cholerae and in some Pseudomonas species. Regulation is achieved by controlling the expression of the acs gene (acetyl-coenzyme A [CoA] synthetase). However, the physiological significance of other identified target genes is not fully understood. Here, we investigated the role of pp_0154 (scpC) and pp_0354/pp_0353 in the soil bacterium Pseudomonas putida KT2440. To this end, the genes were individually deleted and complemented in trans. Then, the growth of the resulting strains on different carbon sources was analyzed. To obtain information on protein function, a bioinformatic analysis was performed, and ScpC was purified and characterized in vitro. Our results indicated that scpC is important for P. putida KT2440 to cope with high concentrations of acetate. The encoded enzyme catalyzes the transfer of coenzyme A between acetate and succinate. On the contrary, pp_0353 and pp_0354 proved to be unimportant for the growth of the strain on acetate under our conditions. Extending the phenotypic analysis to other carbon sources led to the discovery that mxtR, erdR, and pp_0353 are important for the utilization of pyruvate as a carbon source. Taken together, the findings of this study expand the knowledge about the role of the MxtR/ErdR two-component system in carbon source utilization and about the specific functions of its target genes. IMPORTANCE MxtR/ErdR and homologous two-component systems play important roles in the regulatory networks that control cell metabolism and influence bacterial-host interactions. Using the MxtR/ErdR two-component system of the plant growth-promoting soil bacterium Pseudomonas putida KT2440 as a model, this work elucidates the function of previously uncharacterized target genes of MxtR/ErdR and extends the knowledge of the physiological significance of the two-component system. Our results suggest that the target gene scpC encodes an acetate:succinate CoA transferase that is involved in the detoxification of acetate when it is present in large amounts. Furthermore, it is shown that MxtR/ErdR controls the metabolism of not only acetate but also pyruvate. This control involves the target gene pp_0353 (putative exonuclease). These findings may facilitate the optimization of P. putida KT2440 as a chassis for biotechnological applications and may contribute to a better understanding of the regulatory network of pathogens like Pseudomonas aeruginosa.
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Affiliation(s)
- Tania Henríquez
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | - Jyh-Shiuan Hsu
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | | | - Sonja Kuppermann
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | - Michelle Eder
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
| | - Heinrich Jung
- Ludwig-Maximilians-Universität München, Biozentrum, Mikrobiologie, Martinsried, Germany
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Sánchez de la Nieta R, Santamaría RI, Díaz M. Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled. Int J Mol Sci 2022; 23:ijms232315085. [PMID: 36499414 PMCID: PMC9739842 DOI: 10.3390/ijms232315085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria of the Streptomyces genus constitute an authentic biotech gold mine thanks to their ability to produce a myriad of compounds and enzymes of great interest at various clinical, agricultural, and industrial levels. Understanding the physiology of these organisms and revealing their regulatory mechanisms is essential for their manipulation and application. Two-component systems (TCSs) constitute the predominant signal transduction mechanism in prokaryotes, and can detect a multitude of external and internal stimuli and trigger the appropriate cellular responses for adapting to diverse environmental conditions. These global regulatory systems usually coordinate various biological processes for the maintenance of homeostasis and proper cell function. Here, we review the multiple TCSs described and characterized in Streptomyces coelicolor, one of the most studied and important model species within this bacterial group. TCSs are involved in all cellular processes; hence, unravelling the complex regulatory network they form is essential for their potential biotechnological application.
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Involvement of the MxtR/ErdR (CrbS/CrbR) Two-Component System in Acetate Metabolism in Pseudomonas putida KT2440. Microorganisms 2021; 9:microorganisms9081558. [PMID: 34442637 PMCID: PMC8402216 DOI: 10.3390/microorganisms9081558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/20/2022] Open
Abstract
MxtR/ErdR (also called CrbS/CrbR) is a two-component system previously identified as important for the utilization of acetate in Vibrio cholerae and some Pseudomonas species. In addition, evidence has been found in Pseudomonas aeruginosa for a role in regulating the synthesis and expression, respectively, of virulence factors such as siderophores and RND transporters. In this context, we investigated the physiological role of the MxtR/ErdR system in the soil bacterium Pseudomonas putida KT2440. To that end, mxtR and erdR were individually deleted and the ability of the resulting mutants to metabolize different carbon sources was analyzed in comparison to wild type. We also assessed the impact of the deletions on siderophore production, expression of mexEF-oprN (RND transporter), and the biocontrol properties of the strain. Furthermore, the MxtR/ErdR-dependent expression of putative target genes and binding of ErdR to respective promoter regions were analyzed. Our results indicated that the MxtR/ErdR system is active and essential for acetate utilization in P. putida KT2440. Expression of scpC, pp_0354, and acsA-I was stimulated by acetate, while direct interactions of ErdR with the promoter regions of the genes scpC, pp_0354, and actP-I were demonstrated by an electromobility shift assay. Finally, our results suggested that MxtR/ErdR is neither involved in regulating siderophore production nor the expression of mexEF-oprN in P. putida KT2440 under the conditions tested.
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Alves R, Salvadó B, Milo R, Vilaprinyo E, Sorribas A. Maximization of information transmission influences selection of native phosphorelay architectures. PeerJ 2021; 9:e11558. [PMID: 34178454 PMCID: PMC8199921 DOI: 10.7717/peerj.11558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/12/2021] [Indexed: 01/28/2023] Open
Abstract
Phosphorelays are signal transduction circuits that sense environmental changes and adjust cellular metabolism. Five different circuit architectures account for 99% of all phosphorelay operons annotated in over 9,000 fully sequenced genomes. Here we asked what biological design principles, if any, could explain selection among those architectures in nature. We began by studying kinetically well characterized phosphorelays (Spo0 of Bacillus subtilis and Sln1 of Saccharomyces cerevisiae). We find that natural circuit architecture maximizes information transmission in both cases. We use mathematical models to compare information transmission among the architectures for a realistic range of concentration and parameter values. Mapping experimentally determined phosphorelay protein concentrations onto that range reveals that the native architecture maximizes information transmission in sixteen out of seventeen analyzed phosphorelays. These results suggest that maximization of information transmission is important in the selection of native phosphorelay architectures, parameter values and protein concentrations.
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Affiliation(s)
- Rui Alves
- Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Baldiri Salvadó
- Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Ron Milo
- Plant and Environmental Science, Weizmann Institute of Science, Rehovot, Israel
| | - Ester Vilaprinyo
- Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Albert Sorribas
- Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
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Singh D, Gupta P, Singla-Pareek SL, Siddique KHM, Pareek A. The Journey from Two-Step to Multi-Step Phosphorelay Signaling Systems. Curr Genomics 2021; 22:59-74. [PMID: 34045924 PMCID: PMC8142344 DOI: 10.2174/1389202921666210105154808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/21/2020] [Accepted: 12/18/2020] [Indexed: 11/22/2022] Open
Abstract
Background The two-component signaling (TCS) system is an important signal transduction machinery in prokaryotes and eukaryotes, excluding animals, that uses a protein phosphorylation mechanism for signal transmission. Conclusion Prokaryotes have a primitive type of TCS machinery, which mainly comprises a membrane-bound sensory histidine kinase (HK) and its cognate cytoplasmic response regulator (RR). Hence, it is sometimes referred to as two-step phosphorelay (TSP). Eukaryotes have more sophisticated signaling machinery, with an extra component - a histidine-containing phosphotransfer (HPT) protein that shuttles between HK and RR to communicate signal baggage. As a result, the TSP has evolved from a two-step phosphorelay (His–Asp) in simple prokaryotes to a multi-step phosphorelay (MSP) cascade (His–Asp–His–Asp) in complex eukaryotic organisms, such as plants, to mediate the signaling network. This molecular evolution is also reflected in the form of considerable structural modifications in the domain architecture of the individual components of the TCS system. In this review, we present TCS system's evolutionary journey from the primitive TSP to advanced MSP type across the genera. This information will be highly useful in designing the future strategies of crop improvement based on the individual members of the TCS machinery.
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Affiliation(s)
- Deepti Singh
- 1Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; 2Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; 3The UWA Institute of Agriculture, The University of Western Australia, Perth WA 6001, Australia; 4National Agri-Food Biotechnology Institute, Punjab, Ajitgarh 140306, India
| | - Priyanka Gupta
- 1Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; 2Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; 3The UWA Institute of Agriculture, The University of Western Australia, Perth WA 6001, Australia; 4National Agri-Food Biotechnology Institute, Punjab, Ajitgarh 140306, India
| | - Sneh Lata Singla-Pareek
- 1Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; 2Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; 3The UWA Institute of Agriculture, The University of Western Australia, Perth WA 6001, Australia; 4National Agri-Food Biotechnology Institute, Punjab, Ajitgarh 140306, India
| | - Kadambot H M Siddique
- 1Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; 2Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; 3The UWA Institute of Agriculture, The University of Western Australia, Perth WA 6001, Australia; 4National Agri-Food Biotechnology Institute, Punjab, Ajitgarh 140306, India
| | - Ashwani Pareek
- 1Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; 2Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; 3The UWA Institute of Agriculture, The University of Western Australia, Perth WA 6001, Australia; 4National Agri-Food Biotechnology Institute, Punjab, Ajitgarh 140306, India
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Yang Y, Lang N, Zhang L, Wu H, Jiang W, Gu Y. A novel regulatory pathway consisting of a two-component system and an ABC-type transporter contributes to butanol tolerance in Clostridium acetobutylicum. Appl Microbiol Biotechnol 2020; 104:5011-5023. [DOI: 10.1007/s00253-020-10555-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/23/2020] [Accepted: 03/16/2020] [Indexed: 11/28/2022]
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Lesne E, Dupré E, Locht C, Antoine R, Jacob-Dubuisson F. Conformational Changes of an Interdomain Linker Mediate Mechanical Signal Transmission in Sensor Kinase BvgS. J Bacteriol 2017; 199:e00114-17. [PMID: 28507245 PMCID: PMC5573084 DOI: 10.1128/jb.00114-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/08/2017] [Indexed: 11/20/2022] Open
Abstract
The whooping cough agent, Bordetella pertussis, controls the expression of its large virulence regulon in a coordinated manner through the two-component system BvgAS. BvgS is a dimeric, multidomain sensor kinase. Each monomer comprises, in succession, tandem periplasmic Venus flytrap (VFT) domains, a transmembrane segment, a cytoplasmic Per-Arnt-Sim (PAS) domain, a kinase module, and additional phosphorelay domains. BvgS shifts between kinase and phosphatase modes of activity in response to chemical modulators that modify the clamshell motions of the VFT domains. We have shown previously that this regulation involves a shift between distinct states of conformation and dynamics of the two-helix coiled-coil linker preceding the enzymatic module. In this work, we determined the mechanism of signal transduction across the membrane via a first linker, which connects the VFT and PAS domains of BvgS, using extensive cysteine cross-linking analyses and other approaches. Modulator perception by the periplasmic domains appears to trigger a small, symmetrical motion of the transmembrane segments toward the periplasm, causing rearrangements of the noncanonical cytoplasmic coiled coil that follows. As a consequence, the interface of the PAS domains is modified, which affects the second linker and eventually causes the shift of enzymatic activity. The major features of this first linker are well conserved among BvgS homologs, indicating that the mechanism of signal transduction unveiled here is likely to be generally relevant for this family of sensor kinases.IMPORTANCEBordetella pertussis produces virulence factors coordinately regulated by the two-component system BvgAS. BvgS is a sensor kinase, and BvgA is a response regulator that activates gene transcription when phosphorylated by BvgS. Sensor kinases homologous to BvgS are also found in other pathogens. Our goal is to decipher the mechanisms of BvgS signaling, since these sensor kinases may represent new targets for antibacterial agents. Signal perception by the sensor domains of BvgS triggers small motions of the helical linker region underneath. The protein domain that follows this linker undergoes a large conformational change that amplifies the initial signal, causing a shift of activity from kinase to phosphatase. Because BvgS homologs harbor similar regions, these signaling mechanisms are likely to apply generally to that family of sensor kinases.
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Affiliation(s)
- Elodie Lesne
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Elian Dupré
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Camille Locht
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Rudy Antoine
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Françoise Jacob-Dubuisson
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
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8
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Linearmycins Activate a Two-Component Signaling System Involved in Bacterial Competition and Biofilm Morphology. J Bacteriol 2017; 199:JB.00186-17. [PMID: 28461449 DOI: 10.1128/jb.00186-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria use two-component signaling systems to adapt and respond to their competitors and changing environments. For instance, competitor bacteria may produce antibiotics and other bioactive metabolites and sequester nutrients. To survive, some species of bacteria escape competition through antibiotic production, biofilm formation, or motility. Specialized metabolite production and biofilm formation are relatively well understood for bacterial species in isolation. How bacteria control these functions when competitors are present is not well studied. To address fundamental questions relating to the competitive mechanisms of different species, we have developed a model system using two species of soil bacteria, Bacillus subtilis and Streptomyces sp. strain Mg1. Using this model, we previously found that linearmycins produced by Streptomyces sp. strain Mg1 cause lysis of B. subtilis cells and degradation of colony matrix. We identified strains of B. subtilis with mutations in the two-component signaling system yfiJK operon that confer dual phenotypes of specific linearmycin resistance and biofilm morphology. We determined that expression of the ATP-binding cassette (ABC) transporter yfiLMN operon, particularly yfiM and yfiN, is necessary for biofilm morphology. Using transposon mutagenesis, we identified genes that are required for YfiLMN-mediated biofilm morphology, including several chaperones. Using transcriptional fusions, we found that YfiJ signaling is activated by linearmycins and other polyene metabolites. Finally, using a truncated YfiJ, we show that YfiJ requires its transmembrane domain to activate downstream signaling. Taken together, these results suggest coordinated dual antibiotic resistance and biofilm morphology by a single multifunctional ABC transporter promotes competitive fitness of B. subtilisIMPORTANCE DNA sequencing approaches have revealed hitherto unexplored diversity of bacterial species in a wide variety of environments that includes the gastrointestinal tract of animals and the rhizosphere of plants. Interactions between different species in bacterial communities have impacts on our health and industry. However, many approaches currently used to study whole bacterial communities do not resolve mechanistic details of interspecies interactions, including how bacteria sense and respond to their competitors. Using a competition model, we have uncovered dual functions for a previously uncharacterized two-component signaling system involved in specific antibiotic resistance and biofilm morphology. Insights gleaned from signaling within interspecies interaction models build a more complete understanding of gene functions important for bacterial communities and will enhance community-level analytical approaches.
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Diomandé SE, Doublet B, Vasaï F, Guinebretière MH, Broussolle V, Brillard J. Expression of the genes encoding the CasK/R two-component system and the DesA desaturase during Bacillus cereus cold adaptation. FEMS Microbiol Lett 2016; 363:fnw174. [PMID: 27435329 DOI: 10.1093/femsle/fnw174] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 11/13/2022] Open
Abstract
Two-component systems (TCS) allow a cell to elaborate a variety of adaptive responses to environment changes. The recently discovered CasK/R TCS plays a role in the optimal unsaturation of fatty acids necessary for cold adaptation of the foodborne-pathogen Bacillus cereus Here, we showed that the promoter activity of the operon encoding this TCS was repressed during growth at low temperature in the stationary phase in the parental strain when compared to the casK/R mutant, suggesting that CasR negatively regulates the activity of its own promoter in these conditions. The promoter activity of the desA gene encoding the Δ5 fatty acid desaturase, providing unsaturated fatty acids (UFAs) required for low temperature adaptation, was repressed in the casK/R mutant grown at 12°C versus 37°C. This result suggests that CasK/R activates desA expression during B. cereus growth at low temperature, allowing an optimal unsaturation of the fatty acids. In contrast, desA expression was repressed during the lag phase at low temperature in presence of UFAs, in a CasK/R-independent manner. Our findings confirm that the involvement of this major TCS in B. cereus cold adaptation is linked to the upregulation of a fatty acid desaturase.
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Affiliation(s)
| | | | | | | | | | - Julien Brillard
- SQPOV, INRA, Univ. Avignon, 84000 Avignon, France DGIMI, INRA, Univ. Montpellier, 34095 Montpellier, France
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Lesne E, Krammer EM, Dupre E, Locht C, Lensink MF, Antoine R, Jacob-Dubuisson F. Balance between Coiled-Coil Stability and Dynamics Regulates Activity of BvgS Sensor Kinase in Bordetella. mBio 2016; 7:e02089. [PMID: 26933056 PMCID: PMC4810494 DOI: 10.1128/mbio.02089-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/28/2016] [Indexed: 11/24/2022] Open
Abstract
UNLABELLED The two-component system BvgAS controls the expression of the virulence regulon of Bordetella pertussis. BvgS is a prototype of bacterial sensor kinases with extracytoplasmic Venus flytrap perception domains. Following its transmembrane segment, BvgS harbors a cytoplasmic Per-Arnt-Sim (PAS) domain and then a predicted 2-helix coiled coil that precede the dimerization-histidine-phosphotransfer domain of the kinase. BvgS homologs have a similar domain organization, or they harbor only a predicted coiled coil between the transmembrane and the dimerization-histidine-phosphotransfer domains. Here, we show that the 2-helix coiled coil of BvgS regulates the enzymatic activity in a mechanical manner. Its marginally stable hydrophobic interface enables a switch between a state of great rotational dynamics in the kinase mode and a more rigid conformation in the phosphatase mode in response to signal perception by the periplasmic domains. We further show that the activity of BvgS is controlled in the same manner if its PAS domain is replaced with the natural α-helical sequences of PAS-less homologs. Clamshell motions of the Venus flytrap domains trigger the shift of the coiled coil's dynamics. Thus, we have uncovered a general mechanism of regulation for the BvgS family of Venus flytrap-containing two-component sensor kinases. IMPORTANCE The two-component system BvgAS of the whooping cough agent Bordetella pertussis regulates the virulence factors necessary for infection in a coordinated manner. BvgS is the prototype of a family of sensor kinase proteins found in major bacterial pathogens. When BvgS functions as a kinase, B. pertussis is virulent, and the bacterium shifts to an avirulent phase after BvgS senses chemicals that make it switch to phosphatase. Our goal is to decipher the signaling mechanisms of BvgS in order to understand virulence regulation in Bordetella, which may lead to new antimicrobial treatments targeting those two-component systems. We discovered that the activity of BvgS is regulated in a mechanical manner. A short region of the protein that precedes the enzymatic domain switches between two states in response to signal perception by other BvgS domains. This switch region is conserved among BvgS homologs, and thus, the regulation uncovered here will likely be relevant for the family.
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Affiliation(s)
- E Lesne
- Université de Lille, INSERM, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - E-M Krammer
- Université de Lille, CNRS, UMR 8576-UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - E Dupre
- Université de Lille, INSERM, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - C Locht
- Université de Lille, INSERM, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - M F Lensink
- Université de Lille, CNRS, UMR 8576-UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - R Antoine
- Université de Lille, INSERM, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - F Jacob-Dubuisson
- Université de Lille, INSERM, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, Lille, France
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Salvado B, Vilaprinyo E, Sorribas A, Alves R. A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes. PeerJ 2015; 3:e1183. [PMID: 26339559 PMCID: PMC4558063 DOI: 10.7717/peerj.1183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/23/2015] [Indexed: 12/17/2022] Open
Abstract
Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.
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Affiliation(s)
- Baldiri Salvado
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain
| | - Ester Vilaprinyo
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain ; IRBLleida , Lleida, Catalonya , Spain
| | - Albert Sorribas
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain
| | - Rui Alves
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain
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Liu Z, Liu P, Liu S, Song H, Tang H, Hu X. Small protein B upregulates sensor kinase bvgS expression in Aeromonas veronii. Front Microbiol 2015; 6:579. [PMID: 26136727 PMCID: PMC4468919 DOI: 10.3389/fmicb.2015.00579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/26/2015] [Indexed: 01/24/2023] Open
Abstract
Earlier studies reveal that Small protein B (SmpB), a class of well-conserved tmRNA-binding proteins, is essential for the trans-translation process, which functions as a system for translation surveillance and ribosome rescue. Here, we report a previously unrecognized mechanism by which SmpB alone positively regulates the expression of a sensor kinase, BvgS, in Aeromonas veronii. A reporter plasmid was constructed in which the promoter of bvgS was used to control the expression of the enhanced green fluorescent protein (eGFP) gene. When the reporter plasmid was co-transformed with a SmpB expression construct into E. coli, the relative fluorescence intensity increased about threefold. Transformation with a truncated form of smpB gene showed that the C-terminus had little effect, while N-terminus unexpectedly increased eGFP production. Next, a series of SmpB mutants were generated by site-directed mutagenesis. When the mutants SmpB (G11S) or SmpB (E32AG) was used in the experiment, eGFP expression dropped significantly compared with that of wild type SmpB. Further, purified SmpB was shown to bind the promoter regions of bvgS in the agarose gel retardation assay. Quantitative RT-PCR analysis showed that eGFP transcript levels increased approximately 25-fold in the presence of SmpB. Likewise, smpB knockout decreased bvgS transcripts significantly in A. veronii, and also displayed a reduced capability in salt tolerance. Collectively, the data presented here will facilitate a deeper understanding of SmpB-mediated regulatory circuits as a transcriptional factor in A. veronii.
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Affiliation(s)
- Zhu Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Peng Liu
- Department of Biology, College of Sciences, Shantou University Shantou, China
| | - Shuanshuan Liu
- Department of Biology, College of Sciences, Shantou University Shantou, China
| | - Haichao Song
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Hongqian Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Xinwen Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
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Dupré E, Herrou J, Lensink MF, Wintjens R, Vagin A, Lebedev A, Crosson S, Villeret V, Locht C, Antoine R, Jacob-Dubuisson F. Virulence regulation with Venus flytrap domains: structure and function of the periplasmic moiety of the sensor-kinase BvgS. PLoS Pathog 2015; 11:e1004700. [PMID: 25738876 PMCID: PMC4352136 DOI: 10.1371/journal.ppat.1004700] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 11/23/2022] Open
Abstract
Two-component systems (TCS) represent major signal-transduction pathways for adaptation to environmental conditions, and regulate many aspects of bacterial physiology. In the whooping cough agent Bordetella pertussis, the TCS BvgAS controls the virulence regulon, and is therefore critical for pathogenicity. BvgS is a prototypical TCS sensor-kinase with tandem periplasmic Venus flytrap (VFT) domains. VFT are bi-lobed domains that typically close around specific ligands using clamshell motions. We report the X-ray structure of the periplasmic moiety of BvgS, an intricate homodimer with a novel architecture. By combining site-directed mutagenesis, functional analyses and molecular modeling, we show that the conformation of the periplasmic moiety determines the state of BvgS activity. The intertwined structure of the periplasmic portion and the different conformation and dynamics of its mobile, membrane-distal VFT1 domains, and closed, membrane-proximal VFT2 domains, exert a conformational strain onto the transmembrane helices, which sets the cytoplasmic moiety in a kinase-on state by default corresponding to the virulent phase of the bacterium. Signaling the presence of negative signals perceived by the periplasmic domains implies a shift of BvgS to a distinct state of conformation and activity, corresponding to the avirulent phase. The response to negative modulation depends on the integrity of the periplasmic dimer, indicating that the shift to the kinase-off state implies a concerted conformational transition. This work lays the bases to understand virulence regulation in Bordetella. As homologous sensor-kinases control virulence features of diverse bacterial pathogens, the BvgS structure and mechanism may pave the way for new modes of targeted therapeutic interventions.
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Affiliation(s)
- Elian Dupré
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Julien Herrou
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Marc F. Lensink
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, France
| | - René Wintjens
- Laboratory of Biopolymers and Supramolecular Nanomaterials, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexey Vagin
- Structural Biology Laboratory, University of York, York, England, United Kingdom
| | - Andrey Lebedev
- Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Didcot, England, United Kingdom
| | - Sean Crosson
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Vincent Villeret
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, France
| | - Camille Locht
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Rudy Antoine
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Françoise Jacob-Dubuisson
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
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Kim HJ, Jeong H, Hwang S, Lee MS, Lee YJ, Lee DW, Lee SJ. Short-term differential adaptation to anaerobic stress via genomic mutations by Escherichia coli strains K-12 and B lacking alcohol dehydrogenase. Front Microbiol 2014; 5:476. [PMID: 25250024 PMCID: PMC4158980 DOI: 10.3389/fmicb.2014.00476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/25/2014] [Indexed: 01/01/2023] Open
Abstract
Microbial adaptations often occur via genomic mutations under adverse environmental conditions. This study used Escherichia coli ΔadhE cells as a model system to investigate adaptation to anaerobic conditions, which we then compared with the adaptive mechanisms of two closely related E. coli strains, K-12 and B. In contrast to K-12 ΔadhE cells, the E. coli B ΔadhE cells exhibited significantly delayed adaptive growth under anaerobic conditions. Adaptation by the K-12 and B strains mainly employed anaerobic lactate fermentation to restore cellular growth. Several mutations were identified in the pta or pflB genes of adapted K-12 cells, but mostly in the pta gene of the B strains. However, the types of mutation in the adapted K-12 and B strains were similar. Cellular viability was affected directly by severe redox imbalance in B ΔadhE cells, which also impaired their ability to adapt to anaerobic conditions. This study demonstrates that closely related microorganisms may undergo different adaptations under the same set of adverse conditions, which might be associated with the specific metabolic characteristics of each strain. This study provides new insights into short-term microbial adaptation to stressful conditions, which may reflect dynamic microbial population changes in nature.
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Affiliation(s)
- Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and Technology (UST) Daejeon, South Korea ; Infection and Immunity Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Haeyoung Jeong
- Biosystems and Bioengineering Program, University of Science and Technology (UST) Daejeon, South Korea ; Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Moo-Seung Lee
- Infection and Immunity Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Yong-Jik Lee
- School of Applied Biosciences, Kyungpook National University Daegu, South Korea
| | - Dong-Woo Lee
- School of Applied Biosciences, Kyungpook National University Daegu, South Korea
| | - Sang Jun Lee
- Biosystems and Bioengineering Program, University of Science and Technology (UST) Daejeon, South Korea ; Infection and Immunity Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
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Chen L, Wu L, Wang J, Zhang W. Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:89. [PMID: 24932218 PMCID: PMC4057619 DOI: 10.1186/1754-6834-7-89] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Butanol production directly from CO2 in photosynthetic cyanobacteria is restricted by the high toxicity of butanol to the hosts. In previous studies, we have found that a few two-component signal transduction systems (TCSTSs) were differentially regulated in Synechocystis sp. PCC 6803 after butanol treatment. RESULTS To explore regulatory mechanisms of butanol tolerance, in this work, by constructing gene knockout mutants of the butanol-responsive TCSTS genes and conducting tolerance analysis, we uncovered that an orphan slr1037 gene encoding a novel response regulator was involved in butanol tolerance in Synechocystis. Interestingly, the ∆slr1037 mutant grew similarly to the wild type under several other stress conditions tested, which suggests that its regulation on butanol tolerance is specific. Using a quantitative iTRAQ LC-MS/MS proteomics approach coupled with real-time reverse transcription PCR, we further determined the possible butanol-tolerance regulon regulated by Slr1037. The results showed that, after slr1037 deletion, proteins involved in photosynthesis and glycolysis/gluconeogenesis of central metabolic processes, and glutaredoxin, peptide methionine sulfoxide reductase and glucosylglycerol-phosphate synthase with stress-responsive functions were down-regulated, suggesting that Slr1037 may exhibit regulation to a wide range of cellular functions in combating butanol stress. CONCLUSIONS The study provided a proteomic description of the putative butanol-tolerance regulon regulated by the slr1037 gene. As the first signal transduction protein identified directly related to butanol tolerance, response regulator Slr1037 could be a natural candidate for transcriptional engineering to improve butanol tolerance in Synechocystis.
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Affiliation(s)
- Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Lina Wu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Jiangxin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
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16
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Sharma P, Stagge S, Bekker M, Bettenbrock K, Hellingwerf KJ. Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone. PLoS One 2013; 8:e75412. [PMID: 24116043 PMCID: PMC3792059 DOI: 10.1371/journal.pone.0075412] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/14/2013] [Indexed: 01/15/2023] Open
Abstract
Expression of the catabolic network in Escherichia coli is predominantly regulated, via oxygen availability, by the two-component system ArcBA. It has been shown that the kinase activity of ArcB is controlled by the redox state of two critical pairs of cysteines in dimers of the ArcB sensory kinase. Among the cellular components that control the redox state of these cysteines of ArcB are the quinones from the cytoplasmic membrane of the cell, which function in ‘respiratory’ electron transfer. This study is an effort to understand how the redox state of the quinone pool(s) is sensed by the cell via the ArcB kinase. We report the relationship between growth, quinone content, ubiquinone redox state, the level of ArcA phosphorylation, and the level of ArcA-dependent gene expression, in a number of mutants of E. coli with specific alterations in their set of quinones, under a range of physiological conditions. Our results provide experimental evidence for a previously formulated hypothesis that not only ubiquinone, but also demethylmenaquinone, can inactivate kinase activity of ArcB. Also, in a mutant strain that only contains demethylmenaquinone, the extent of ArcA phosphorylation can be modulated by the oxygen supply rate, which shows that demethylmenaquinone can also inactivate ArcB in its oxidized form. Furthermore, in batch cultures of a strain that contains ubiquinone as its only quinone species, we observed that the ArcA phosphorylation level closely followed the redox state of the ubiquinone/ubiquinol pool, much more strictly than it does in the wild type strain. Therefore, at low rates of oxygen supply in the wild type strain, the activity of ArcB may be inhibited by demethylmenaquinone, in spite of the fact that the ubiquinones are present in the ubiquinol form.
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Affiliation(s)
- Poonam Sharma
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, and Netherlands Institute for Systems Biology, Amsterdam, the Netherlands
| | - Stefan Stagge
- MPI für Dynamik Komplexer Technischer Systeme, Experimentelle Systembiologie, Magdeburg, Germany
| | - Martijn Bekker
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, and Netherlands Institute for Systems Biology, Amsterdam, the Netherlands
| | - Katja Bettenbrock
- MPI für Dynamik Komplexer Technischer Systeme, Experimentelle Systembiologie, Magdeburg, Germany
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, and Netherlands Institute for Systems Biology, Amsterdam, the Netherlands
- * E-mail:
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17
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Manipulation of the anoxic metabolism in Escherichia coli by ArcB deletion variants in the ArcBA two-component system. Appl Environ Microbiol 2012; 78:8784-94. [PMID: 23064346 DOI: 10.1128/aem.02558-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bioprocesses conducted under conditions with restricted O(2) supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative anaerobe Escherichia coli has elaborate sensing and signal transduction mechanisms for redox control in response to the availability of O(2) and other electron acceptors. The ArcBA two-component system consists of ArcB, a membrane-associated sensor kinase, and ArcA, the cognate response regulator. The tripartite hybrid kinase ArcB possesses a transmembrane, a PAS, a primary transmitter (H1), a receiver (D1), and a phosphotransfer (H2) domain. Metabolic fluxes were compared under anoxic conditions in a wild-type E. coli strain, its ΔarcB derivative, and two partial arcB deletion mutants in which ArcB lacked either the H1 domain or the PAS-H1-D1 domains. These analyses revealed that elimination of different segments in ArcB determines a distinctive distribution of d-glucose catabolic fluxes, different from that observed in the ΔarcB background. Metabolite profiles, enzyme activity levels, and gene expression patterns were also investigated in these strains. Relevant alterations were observed at the P-enol-pyruvate/pyruvate and acetyl coenzyme A metabolic nodes, and the formation of reduced fermentation metabolites, such as succinate, d-lactate, and ethanol, was favored in the mutant strains to different extents compared to the wild-type strain. These phenotypic traits were associated with altered levels of the enzymatic activities operating at these nodes, as well as with elevated NADH/NAD(+) ratios. Thus, targeted modification of global regulators to obtain different metabolic flux distributions under anoxic conditions is emerging as an attractive tool for metabolic engineering purposes.
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18
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Sousa PMF, Videira MAM, Bohn A, Hood BL, Conrads TP, Goulao LF, Melo AMP. The aerobic respiratory chain of Escherichia coli: from genes to supercomplexes. MICROBIOLOGY-SGM 2012; 158:2408-2418. [PMID: 22700653 DOI: 10.1099/mic.0.056531-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In spite of the large number of reports on the aerobic respiratory chain of Escherichia coli, from gene transcription regulation to enzyme kinetics and structural studies, an integrative perspective of this pathway is yet to be produced. Here, a multi-level analysis of the aerobic respiratory chain of E. coli was performed to find correlations between gene transcription, enzyme activity, growth dynamics, and supercomplex formation and composition. The transcription level of all genes encoding the aerobic respiratory chain of E. coli varied significantly in response to bacterial growth. Coordinated expression patterns were observed between the genes encoding NADH : quinone oxidoreductase and complex I (NDH-1), alternative NADH : quinone oxidoreductase (NDH-2) and cytochrome bdI, and also between sdhA and appC, encoding succinate dehydrogenase and cytochrome bdII, respectively. In general, the rates of the respiratory chain activities increased from mid-exponential to late-stationary phase, with no significant further variation occurring until the mid-stationary phase. Multi-level correlations between gene transcription, enzyme activity and growth dynamics were also found in this study. The previously reported NADH dehydrogenase and formate : oxygen oxidoreductase supercomplexes of E. coli were already assembled at mid-exponential phase and remained throughout growth. A new succinate oxidase supercomplex composed of succinate dehydrogenase and cytochrome bdII was identified, in agreement with the suggestion provided by the coordinated transcription of sdhA and appC.
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Affiliation(s)
- Pedro M F Sousa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN) 2780-157 Oeiras, Portugal.,Eco-Bio, Instituto de Investigação Científica Tropical, Av. da República (EAN) 2784-505 Oeiras, Portugal
| | - Marco A M Videira
- Eco-Bio, Instituto de Investigação Científica Tropical, Av. da República (EAN) 2784-505 Oeiras, Portugal
| | - Andreas Bohn
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN) 2780-157 Oeiras, Portugal
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Women's Health Integrated Research Center at Inova Health System, Woodburn II, Suite 375, 3289 Woodburn Road, Annandale, VA 22003, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Women's Health Integrated Research Center at Inova Health System, Woodburn II, Suite 375, 3289 Woodburn Road, Annandale, VA 22003, USA
| | - Luis F Goulao
- Eco-Bio, Instituto de Investigação Científica Tropical, Av. da República (EAN) 2784-505 Oeiras, Portugal
| | - Ana M P Melo
- Eco-Bio, Instituto de Investigação Científica Tropical, Av. da República (EAN) 2784-505 Oeiras, Portugal
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19
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Zaoui C, Overhage J, Löns D, Zimmermann A, Müsken M, Bielecki P, Pustelny C, Becker T, Nimtz M, Häussler S. An orphan sensor kinase controls quinolone signal production via MexT in Pseudomonas aeruginosa. Mol Microbiol 2012; 83:536-47. [PMID: 22168309 DOI: 10.1111/j.1365-2958.2011.07947.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa employs both N-acylhomoserine lactone and 2-alkyl-4(1H)-quinolone (AQ)-mediated interbacterial signalling for the orchestration of a genome-wide gene regulatory network. Despite the many advances that have been made in understanding the target genes of quorum sensing regulation, little is known on how quorum sensing systems are influenced by environmental cues. In this study, we show that AQ production is modulated by an orphan P. aeruginosa sensor kinase. Transcriptional studies of the sensor kinase (MxtR) mutant demonstrated that an induced expression of MexT, a LysR-type transcriptional regulator, largely determined the global transcriptional profile. Thereby, overexpression of the MexT-regulated MexEF-OprN efflux pump led to a delayed expression of the AQ biosynthetic genes and of AQ-dependent virulence factors. Furthermore, we demonstrated that autophosphorylation of MxtR was inhibited by ubiquinone, the central electron carrier of respiration in in vitro experiments. Our results elucidate on a mechanism by which P. aeruginosa senses environmental conditions and adapts by controlling the production of interbacterial AQ signal molecules. A regulatory function of a sensor kinase may indicate that there is a pre-emptive role of adaptation mechanisms that are turned on under distinct environmental conditions and that are important for efficient colonization and pathogenesis.
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Affiliation(s)
- Caroline Zaoui
- Chronic Pseudomonas Infection Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
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20
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Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism. Proc Natl Acad Sci U S A 2010; 107:17351-5. [PMID: 20855615 DOI: 10.1073/pnas.1006267107] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two-component sensory transduction systems control important bacterial programs. In Bordetella pertussis, expression of the virulence regulon is controlled by the unorthodox BvgAS two-component system. BvgS is the prototype of a family of sensor-kinases that harbor periplasmic domains homologous to bacterial solute-binding proteins. Although BvgAS is active under laboratory conditions, no activating signal has been identified, only negative modulators. Here we show that the second periplasmic domain of BvgS interacts with modulators and adopts a Venus flytrap (VFT) fold. X-ray crystallography reveals that the two lobes of VFT2 delimitate a ligand-binding cavity enclosing fortuitous ligands. Most substitutions of putative ligand-binding residues in the VFT2 cavity keep BvgS active, and alteration of the cavity's electrostatic potential affects responsiveness to modulation. The crystal structure of this VFT2 variant conferring constitutive kinase activity to BvgS shows a closed cavity with another nonspecific ligand. Thus, VFT2 is closed and active without a specific agonist ligand, in contrast to typical VFTs. Modulators are antagonists of VFT2 that interrupt signaling. BvgAS is active for most of the B. pertussis infectious cycle, consistent with the proposed mechanism.
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21
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Papenfort K, Said N, Welsink T, Lucchini S, Hinton JCD, Vogel J. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 2009; 74:139-158. [PMID: 19732340 DOI: 10.1111/j.1365-2958.2009.06857.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome-wide screens in Escherichia coli and Salmonella. Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial 'core' small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post-transcriptional regulator in Salmonella, repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl-accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady-state levels of > 16% (> 750) of all Salmonella mRNAs, and rendered the bacteria non-motile. Deep sequencing detected a dramatically changed profile of Hfq-bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post-transcriptional regulation.
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Affiliation(s)
- Kai Papenfort
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Nelly Said
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Tim Welsink
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Sacha Lucchini
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Jay C D Hinton
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Jörg Vogel
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
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Herrou J, Debrie AS, Willery E, Renaud-Mongénie G, Locht C, Mooi F, Jacob-Dubuisson F, Antoine R. Molecular evolution of the two-component system BvgAS involved in virulence regulation in Bordetella. PLoS One 2009; 4:e6996. [PMID: 19750014 PMCID: PMC2737282 DOI: 10.1371/journal.pone.0006996] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 07/27/2009] [Indexed: 11/19/2022] Open
Abstract
The whooping cough agent Bordetella pertussis is closely related to Bordetella bronchiseptica, which is responsible for chronic respiratory infections in various mammals and is occasionally found in humans, and to Bordetella parapertussis, one lineage of which causes mild whooping cough in humans and the other ovine respiratory infections. All three species produce similar sets of virulence factors that are co-regulated by the two-component system BvgAS. We characterized the molecular diversity of BvgAS in Bordetella by sequencing the two genes from a large number of diverse isolates. The response regulator BvgA is virtually invariant, indicating strong functional constraints. In contrast, the multi-domain sensor kinase BvgS has evolved into two different types. The pertussis type is found in B. pertussis and in a lineage of essentially human-associated B. bronchiseptica, while the bronchiseptica type is associated with the majority of B. bronchiseptica and both ovine and human B. parapertussis. BvgS is monomorphic in B. pertussis, suggesting optimal adaptation or a recent population bottleneck. The degree of diversity of the bronchiseptica type BvgS is markedly different between domains, indicating distinct evolutionary pressures. Thus, absolute conservation of the putative solute-binding cavities of the two periplasmic Venus Fly Trap (VFT) domains suggests that common signals are perceived in all three species, while the external surfaces of these domains vary more extensively. Co-evolution of the surfaces of the two VFT domains in each type and domain swapping experiments indicate that signal transduction in the periplasmic region may be type-specific. The two distinct evolutionary solutions for BvgS confirm that B. pertussis has emerged from a specific B. bronchiseptica lineage. The invariant regions of BvgS point to essential parts for its molecular mechanism, while the variable regions may indicate adaptations to different lifestyles. The repertoire of BvgS sequences will pave the way for functional analyses of this prototypic system.
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Affiliation(s)
- Julien Herrou
- Institut National de la Santé Et de la Recherche Médicale (INSERM-U629), Lille, France
- Institut Fédératif de Recherche (IFR142), Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Anne-Sophie Debrie
- Institut National de la Santé Et de la Recherche Médicale (INSERM-U629), Lille, France
- Institut Fédératif de Recherche (IFR142), Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Eve Willery
- Institut National de la Santé Et de la Recherche Médicale (INSERM-U629), Lille, France
- Institut Fédératif de Recherche (IFR142), Lille, France
- Institut Pasteur de Lille, Lille, France
| | | | - Camille Locht
- Institut National de la Santé Et de la Recherche Médicale (INSERM-U629), Lille, France
- Institut Fédératif de Recherche (IFR142), Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Frits Mooi
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Françoise Jacob-Dubuisson
- Institut National de la Santé Et de la Recherche Médicale (INSERM-U629), Lille, France
- Institut Fédératif de Recherche (IFR142), Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Rudy Antoine
- Institut National de la Santé Et de la Recherche Médicale (INSERM-U629), Lille, France
- Institut Fédératif de Recherche (IFR142), Lille, France
- Institut Pasteur de Lille, Lille, France
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Vitale E, Milani A, Renzi F, Galli E, Rescalli E, de Lorenzo V, Bertoni G. Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma54-promoter Pu to the response regulator PprA. Mol Microbiol 2009; 69:698-713. [PMID: 19138193 DOI: 10.1111/j.1365-2958.2008.06321.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Implantation of the regulatory circuit of the degradation pathway of TOL plasmid pWW0 in the native transcriptional network of the host Pseudomonas putida involves interplay between plasmid- and chromosome-encoded factors. We have employed a reverse genetics approach to investigate such a molecular wiring by identifying host proteins that form stable complexes with Pu, the sigma(54)-dependent promoter of the upper TOL operon of pWW0. This approach revealed that the Pu upstream activating sequences (UAS), the target sites of the cognate activator XylR, form a specific complex with a host protein which, following DNA affinity purification and mass spectrometry analysis, was identified as the LytTR-type two-component response regulator PprA. Directed inactivation of pprA resulted in the upregulation of the Pu promoter in vivo, while expression of the same gene from a plasmid vector strongly repressed Pu activity. Such a downregulation of Pu by PprA could be faithfully reproduced both in vitro with purified components and in an in vivo reporter system assembled in Escherichia coli. The overlap of the PprA and XylR binding sites suggested that the basis for the inhibitory effect on Pu was a mutual exclusion mechanism between the two proteins to bind the UAS. We argue that the binding of the response regulator PprA to Pu (a case without precedents in sigma(54)-dependent transcription) helps to anchor the TOL regulatory subnetwork to the wider context of the host transcriptome, thereby allowing the entry of physiological signals that modulate the outcome of promoter activity.
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Affiliation(s)
- Elena Vitale
- Department of Biomolecular Sciences and Biotechnology, University of Milan, Milan, Italy
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Schnell R, Agren D, Schneider G. 1.9 A structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:1096-100. [PMID: 19052358 PMCID: PMC2593691 DOI: 10.1107/s1744309108035203] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 10/28/2008] [Indexed: 11/10/2022]
Abstract
NarL from Mycobacterium tuberculosis is a putative nitrate response regulator that is involved in the regulation of anaerobic metabolism in this pathogen. The recombinant purified N-terminal signal receiver domain of NarL has been crystallized in space group C222(1), with unit-cell parameters a = 85.6, b = 90.0, c = 126.3 A, and the structure was determined by molecular replacement to 1.9 A resolution. Comparisons with related signal receiver domains show that the closest structural homologue is an uncharacterized protein from Staphylococcus aureus, whereas the nearest sequence homologue, NarL from Escherichia coli, displays larger differences in three-dimensional structure. The largest differences between the mycobacterial and E. coli NarL domains were found in the loop between beta3 and alpha3 in the proximity of the phosphorylation site. The active site in response regulators is similar to that of members of the haloacid dehalogenase (HAD) family, which also form a phospho-aspartyl intermediate. In NarL, the aspartic acid that acts as catalytic acid/base in several HAD enzymes is replaced by an arginine residue, which is less likely to participate in steps involving proton abstraction. This substitution may slow down the breakdown of the phospho-aspartyl anhydride and allow signalling beyond the timescales defined by a catalytic reaction intermediate.
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Affiliation(s)
- Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
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Master and commander in fungal pathogens: the two-component system and the HOG signaling pathway. EUKARYOTIC CELL 2008; 7:2017-36. [PMID: 18952900 DOI: 10.1128/ec.00323-08] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Denton AM, Wu J, Townsend MK, Sule P, Prüss BM. Relating gene expression data on two-component systems to functional annotations in Escherichia coli. BMC Bioinformatics 2008; 9:294. [PMID: 18578884 PMCID: PMC2478693 DOI: 10.1186/1471-2105-9-294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 06/25/2008] [Indexed: 11/30/2022] Open
Abstract
Background Obtaining physiological insights from microarray experiments requires computational techniques that relate gene expression data to functional information. Traditionally, this has been done in two consecutive steps. The first step identifies important genes through clustering or statistical techniques, while the second step assigns biological functions to the identified groups. Recently, techniques have been developed that identify such relationships in a single step. Results We have developed an algorithm that relates patterns of gene expression in a set of microarray experiments to functional groups in one step. Our only assumption is that patterns co-occur frequently. The effectiveness of the algorithm is demonstrated as part of a study of regulation by two-component systems in Escherichia coli. The significance of the relationships between expression data and functional annotations is evaluated based on density histograms that are constructed using product similarity among expression vectors. We present a biological analysis of three of the resulting functional groups of proteins, develop hypotheses for further biological studies, and test one of these hypotheses experimentally. A comparison with other algorithms and a different data set is presented. Conclusion Our new algorithm is able to find interesting and biologically meaningful relationships, not found by other algorithms, in previously analyzed data sets. Scaling of the algorithm to large data sets can be achieved based on a theoretical model.
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Affiliation(s)
- Anne M Denton
- Department of Computer Science and Operations Research, North Dakota State University, Fargo, ND 58105, USA.
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Wang L, Xu G, Chen H, Zhao Y, Xu N, Tian B, Hua Y. DrRRA: a novel response regulator essential for the extreme radioresistance of Deinococcus radiodurans. Mol Microbiol 2008; 67:1211-22. [DOI: 10.1111/j.1365-2958.2008.06113.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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28
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Marles-Wright J, Lewis RJ. Stress responses of bacteria. Curr Opin Struct Biol 2007; 17:755-60. [DOI: 10.1016/j.sbi.2007.08.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
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